Table 1.

RNAseq statistics for I. ricinus IRE/CTVM20 cells, uninfected at 0 hpi, or infected with LIV or TBEV at 168 hpi (upper panel), and differential gene expression statistics at 168 hpi following infection with LIV or TBEV at 0 hpi, compared to uninfected cells at 0 hpi (lower panel)

Parameter	Uninfected 0 hpi (replicate 1/replicate 2)	LIV 168 hpi (replicate 1/replicate 2)	TBEV 168 hpi (replicate 1/replicate 2)
Total reads	11,976,631/10,334,781	16,075,150/13,693,034	13,339,640/18,910,604
Aligned reads	11,976,631/10,334,781	16,075,150/13,693,034	13,339,640/18,910,604
PF_reads	11,976,631/10,334,781	16,075,150/13,693,034	13,339,640/18,910,604
PF_aligned reads	11,976,631/10,334,781	16,075,150/13,693,034	13,339,640/18,910,604
PF_HQ_aligned reads	3,878,432/3,760,670	4,956,000/3,983,347	4,775,958/6,552,021
Mean read length	119/119	119/119	119/119
PF_HQ_error rate	0.76256/0.76193	0.763221/0.764392	0.766099/0.765034
PF_indel rate	0.000667/0.000668	0.0007/0.000667	0.000629/0.000636
Total genes annotated	na	20,861	20,861
Total DE genes	na	613 (2.96%)	409 (1.98%)
Upregulated DE genes	na	402 (65.6%)	252 (61.6%)
Downregulated DE genes	na	211 (34.4%)	157 (38.4%)

Abbreviations: na not available, HPI hours post-infection, PF pass-Illumina filter, HQ high quality, PF_HQ_ERROR_RATE percentage of I. ricinus sequence bases that mismatch the I. scapularis reference genome sequence in PF HQ aligned reads, PF_INDEL_RATE number of insertion and deletion events per 100 PF aligned bases. This uses the number of events as the numerator, not the number of inserted or deleted bases. Picard metrics definitions (https://broadinstitute.github.io/picard/picard-metric-definitions.html) were used, DE differentially expressed